Mitochondria are unusual among the organelles of a eukaryotic cell in that they possess their own genome, the mtDNA. The replication and transcription of mtDNA and the translation of the mtDNA- encoded proteins is essential for the production of ATP by oxidative phosphorylation. Evolutionary analyses and molecular studies of human mtDNA indicate that recombination of human mtDNA occurs. Recombination of mtDNA occurs at low levels in healthy individuals and results in the accumulation of mtDNA rearrangements, whose levels increase with age. At high levels, mtDNA rearrangements can result in mitochondrial dysfunction and human disease. It is difficult to observe mtDNA recombination experimentally in cells because of the lack of appropriate mtDNA markers to detect recombination. A model system is described here that uses uniquely marked human mtDNAs that permit the detection of inter-molecular and intra-molecular recombinant mtDNAs. This system of analysis will be used to identify the products of mtDNA recombination and to determine their rates of formation. Subsequently, the mechanisms by which recombinant mtDNAs are formed in cells will be investigated. These investigations are likely to lead to significant,insights into the mechanism for formation of pathogenic mtDNA rearrangements, as well as into fundamental cellular processes involving mtDNA including mtDNA maintenance, replication, and repair mechanisms.